Research workbench

Aaa-ATPase ring of pan-proteasomes

Analyse Aaa-ATPase ring of pan-proteasomes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HE4
Type: protein
Length: 1,602 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteasome-activating nucleotidase
UniProt: O28303
Ligands: ATP, ADP, MG
Pockets: 17 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 45% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, I, K, L, M, J	Proteasome-activating nucleotidase	protein	267	45% helix, 8% strand	O28303

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains H, I, J, K, L
ADP · Adenosine-5'-diphosphate · ligand · chains L, M
MG · Magnesium ion · metal · 5 copies · chains H, I, J, K, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1003	0.83	0.84	101	ADP, MG
2	327	0.83	0.93	48	ATP, MG
3	440	0.82	0.89	56	ATP, MG
4	974	0.81	0.82	105	ATP, MG
5	497	0.79	0.86	56	ATP, MG

Interfaces

14 interfaces between chains.

K–J · 2563 Å² buried · 26 hydrogen bonds · protein-protein
I–J · 2367 Å² buried · 29 hydrogen bonds · protein-protein
H–I · 2313 Å² buried · 21 hydrogen bonds · protein-protein
K–L · 2252 Å² buried · 22 hydrogen bonds · protein-protein
L–M · 1901 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6HE4 · AAA-ATPase ring of PAN-proteasomes · the same entry in another collection · chain K against K, TM-score 1.00
O28303 · AlphaFold monomer V2.0 prediction for proteasome-activating nucleotidase (O28303) · a predicted model of the same protein · chain H against A, TM-score 0.92

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O28303
Elsewhere: RCSB PDB 6HE4 · PDBe 6HE4 · UniProt O28303

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